\contentsline {lstlisting}{\numberline {1}Example of SNP file format}{6}{lstlisting.1}
\contentsline {lstlisting}{\numberline {2}\textbf {Bottleneck:} At time \lstinline [language=Python, showstringspaces=False]@TF@ + \lstinline [language=Python, showstringspaces=False]@TB@ in the past, an equilibrium population goes through a bottleneck of depth \lstinline [language=Python, showstringspaces=False]@nuB@, recovering to relative size \lstinline [language=Python, showstringspaces=False]@nuF@.}{14}{lstlisting.2}
\contentsline {lstlisting}{\numberline {3}\textbf {Exponential growth:} At time \lstinline [language=Python, showstringspaces=False]@T@ in the past, an equilibrium population begins growing exponentially, reaching size \lstinline [language=Python, showstringspaces=False]@nu@ at present.}{14}{lstlisting.3}
\contentsline {lstlisting}{\numberline {4}\textbf {Split with migration:} At time \lstinline [language=Python, showstringspaces=False]@T@ in the past, two population diverge from an equilibrium population, with relative sizes \lstinline [language=Python, showstringspaces=False]@nu1@ and \lstinline [language=Python, showstringspaces=False]@nu2@ and with symmetric migration at rate \lstinline [language=Python, showstringspaces=False]@m@.}{14}{lstlisting.4}
\contentsline {lstlisting}{\numberline {5}\textbf {Two-population isolation-with-migration:} The ancestral population splits into two, with a fraction \lstinline [language=Python, showstringspaces=False]@s@ going into pop 1 and fraction \lstinline [language=Python, showstringspaces=False]@1-s@ into pop 2. The populations then grow exponentially, with asymmetric migration allowed between them.}{15}{lstlisting.5}
\contentsline {lstlisting}{\numberline {6}\textbf {Out-of-Africa model from Gutenkunst (2009):} This model involves a size change in the ancestral population, a split, another split, and then exponential growth of populations 1 and 2. (The \lstinline [language=Python, showstringspaces=False]@from dadi import@ line imports those modules from the \lstinline [language=Python, showstringspaces=False]@dadi@ namespace into the local namespace, so we don't have to type \lstinline [language=Python, showstringspaces=False]@dadi.@ to access them.)}{16}{lstlisting.6}
\contentsline {lstlisting}{\numberline {7}\textbf {Fixed $\boldsymbol {\theta }$:} A split demographic model function with a fixed value of $\theta $=137 for derived population 1. The free parameters are the sizes of the ancestral pop, \lstinline [language=Python, showstringspaces=False]@nuA@, and derived pop 2, \lstinline [language=Python, showstringspaces=False]@nu2@, (relative to derived pop 1), along with the divergence time \lstinline [language=Python, showstringspaces=False]@T@ between the two derived pops.}{17}{lstlisting.7}
\contentsline {lstlisting}{\numberline {8}\textbf {Settlement-of-New-World model from Gutenkunst (2009):} Because $\partial $a$\partial $i\xspace is limited to 3 simultaneous populations, we need to integrate out the African population, using \lstinline [language=Python, showstringspaces=False]@Numerics.trapz@. This model also employs a fixed $\theta $, and ancillary parameters passed in using the third argument.}{18}{lstlisting.8}
